MSI Repackaging - issues and solutions

I was thinking that it would be nice to have a topic about packaging problems that we encounter and the solutions we found for those problems.
This topic could be useful for those that will encounter them and don't know what to do.

Let me start with SalesLogix Admin Tools and Servers. These days i had to repackage this application and i had a problem with SalesLogix Architect.
If you installed the application and you ran it only on user account (without administrative or power user rights) it won't work. If you first started the application on an administrative account then it worked on a user account also.

This is because at runtime the application generates some entries under HKEY_CLASSES_ROOT. You need to capture these keys. Also you need give some permissions on HKCR\TypeLib\{EF244DC7-4E50-4C30-9237-A3C82A7B2AF6}.
It seems that the application modifies this TypeLib at runtime and in some cases it crashes on the normal user if it doesn't have the needed permissions.